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Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography

Ravikumar, A and Gopnarayan, MN and Subramaniam, S and Srinivasan, N (2022) Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography. In: IUCrJ, 9 . pp. 98-103.

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Official URL: https://doi.org/10.1107/S2052252521011945


An evaluation of systematic differences in local structure and conformation in the interior of protein tertiary structures determined by crystallography and by cryo-electron microscopy (cryo-EM) is reported. The expectation is that any consistent differences between the derived atomic models could provide insights into variations in side-chain packing that result from differences in specimens prepared for analysis between these two methods. By computing an atomic packing score, which provides a quantitative measure of clustering of side-chain atoms in the core of the tertiary structures, it is found that, in general, for structures determined by cryo-EM, side chains are more dispersed than in structures determined by X-ray crystallography over a similar resolution range. This trend is also observed in the packing comparison at subunit interfaces. Similar trends were observed in the packing comparison at the core of tertiary structures of the same proteins determined by both X-ray and cryo-EM methods. It is proposed here that the reduced dispersion of side chains in protein crystals could be due to some level of dehydration in 3D crystals prepared for X-ray crystallography and also because the higher rate of freezing of protein samples for cryo-EM may enable preservation of a more native conformation. © 2022.

Item Type: Journal Article
Publication: IUCrJ
Publisher: International Union of Crystallography
Additional Information: The copyright for this article belongs to International Union of Crystallography
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
UG Programme
Date Deposited: 07 Feb 2022 12:03
Last Modified: 07 Feb 2022 12:03
URI: http://eprints.iisc.ac.in/id/eprint/71183

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